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Diversity, Volume 2, Issue 6 (June 2010), Pages 837-958

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Research

Jump to: Review

Open AccessArticle Genome-Wide Loss of Diversity in the Critically Endangered Hawaiian Monk Seal
Diversity 2010, 2(6), 863-880; doi:10.3390/d2060863
Received: 25 February 2010 / Revised: 19 May 2010 / Accepted: 20 May 2010 / Published: 28 May 2010
Cited by 9 | PDF Full-text (1482 KB) | HTML Full-text | XML Full-text
Abstract
Threatened species often exhibit low genetic diversity as a result of selective sweeps, historical bottlenecks, or persistent small population size. Whereas selective sweeps create localized reduction of variation at a chromosome, population bottlenecks result in the loss of rare alleles throughout the [...] Read more.
Threatened species often exhibit low genetic diversity as a result of selective sweeps, historical bottlenecks, or persistent small population size. Whereas selective sweeps create localized reduction of variation at a chromosome, population bottlenecks result in the loss of rare alleles throughout the genome. Heterozygosity is lost more slowly and is severely impacted only when populations are small for an extended period of time. We test the hypotheses of selective sweep, historical bottleneck and persistently small population size to explain extremely low genetic diversity in the critically endangered Hawaiian monk seal (Monachus schauinslandi). Of 163 microsatellite loci isolated from the species’ genome, only 17 are polymorphic. Mapping 98 monomorphic and 12 polymorphic loci to 35 chromosomes throughout the dog genome, we reject the selective sweep hypothesis. Genotyping 2,423 Hawaiian monk seals at the 17 polymorphic loci plus a locus previously isolated from another pinniped species, we find evidence for a recent bottleneck (P = 0.04). This is consistent with historical records describing intense hunting in the 19th century; however, the bottleneck was not of sufficient severity and duration to explain the genome-wide depletion of genetic diversity (HO = 0.05; A = 1.1). Long-term population size restriction is a more likely explanation. Though at least two of the polymorphic loci appear to be candidates for selection, the low genetic diversity of the species may further threaten chances for survival of this critically endangered species in a changing world. Full article
(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)
Open AccessArticle Coral Ecosystem Resilience, Conservation and Management on the Reefs of Jamaica in the Face of Anthropogenic Activities and Climate Change
Diversity 2010, 2(6), 881-896; doi:10.3390/d2060881
Received: 13 March 2010 / Revised: 26 April 2010 / Accepted: 18 May 2010 / Published: 1 June 2010
Cited by 5 | PDF Full-text (1573 KB) | HTML Full-text | XML Full-text
Abstract
Knowledge of factors that are important in reef resilience and integrity help us understand how reef ecosystems react following major anthropogenic and environmental disturbances. The North Jamaican fringing reefs have shown some recent resilience to acute disturbances from hurricanes and bleaching, in [...] Read more.
Knowledge of factors that are important in reef resilience and integrity help us understand how reef ecosystems react following major anthropogenic and environmental disturbances. The North Jamaican fringing reefs have shown some recent resilience to acute disturbances from hurricanes and bleaching, in addition to the recurring chronic stressors of over-fishing and land development. Factors that can improve coral reef resilience are reviewed, and reef rugosity is shown to correlate with coral cover and growth, particularly for branching Acropora species. The biodiversity index for the Jamaican reefs was lowered after the 2005 mass bleaching event, as were the numbers of coral colonies, but both had recovered by 2009. The importance of coastal zone reef management strategies and the economic value of reefs are discussed, and a protocol is suggested for future management of Jamaican reefs. Full article
(This article belongs to the Special Issue Biodiversity, Conservation and Ecosystem Management)
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Open AccessArticle Diversity or Solidarity? Making Sense of the “New” Social Democracy
Diversity 2010, 2(6), 897-909; doi:10.3390/d2060897
Received: 8 April 2010 / Revised: 10 May 2010 / Accepted: 19 May 2010 / Published: 7 June 2010
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Abstract
One of the key discussions emerging from within the centre and centre-left of British politics is the means of combining a commitment to diversity with the aim of achieving social solidarity. While there has been a populist strand to this debate recently [...] Read more.
One of the key discussions emerging from within the centre and centre-left of British politics is the means of combining a commitment to diversity with the aim of achieving social solidarity. While there has been a populist strand to this debate recently with the contribution of writers such as Goodhart who has argued that diversity specifically undermines the willingness of the majority (white Anglo-Saxons) to pay for collective welfare provision, there has also been recognition of the difficulty of promoting difference and unity from within even the more sympathetic elements of the academic literature. The purpose of this paper is to consider the nature of this dilemma and to propose a tentative solution. In essence we suggest that the problem lies not in creating a fit between the two elements for the sake of making the ‘new’ social democracy work but in rebuilding traditional social democracy. Full article
(This article belongs to the Special Issue Ethnic Diversity and Cultural Pluralism)
Open AccessArticle Microbial Community Composition as Affected by Dryland Cropping Systems and Tillage in a Semiarid Sandy Soil
Diversity 2010, 2(6), 910-931; doi:10.3390/d2060910
Received: 19 April 2010 / Revised: 28 May 2010 / Accepted: 1 June 2010 / Published: 7 June 2010
Cited by 25 | PDF Full-text (1191 KB) | HTML Full-text | XML Full-text
Abstract
This study evaluated microbial communities of soil (0–10 cm) as affected by dryland cropping systems under different tillage practices after 5 years. The soil type was an Olton sandy loam with an average of 16.4% clay, 67.6% sand and 0.65 g kg [...] Read more.
This study evaluated microbial communities of soil (0–10 cm) as affected by dryland cropping systems under different tillage practices after 5 years. The soil type was an Olton sandy loam with an average of 16.4% clay, 67.6% sand and 0.65 g kg−1 of organic matter (OM). The cropping systems evaluated were grain sorghum (Sorghum bicolor L.)—cotton (Gossypium hirsutum) (Srg-Ct), cotton-winter rye (Secale cereale)-grain sorghum (Ct-Rye-Srg), and a rotation of forage (f) sorghum (Sorghum bicolor L. and Sorghum sudanense) with winter rye (Srf-Rye), which were under no-tillage (nt) and conventional tillage (ct) practices. Soil microbial communities under cotton based cropping systems (Srg-Ct and Ct-Rye-Srg) showed lower fungal:bacterial ratios compared to the soil under Srf-Rye. Soil under Srf-Rye showed higher population densities of Bacteroidetes and Proteobacteria while lower Actinobacteria compared to Srg-Ct and Ct-Rye-Srg. Chloroflexi, Gemmatimonadetes and Verrucomicrobiae were higher in tilled soil compared to the no-tilled plots. Regardless the limited irrigation available to sustain agricultural production within these dryland cropping systems, this study demonstrated that differences in microbial communities are more affected by crop rotation than tillage management history. Although soil fungal diversity was not analyzed in this study, pyrosequencing suggests that tillage practices can affect bacterial phyla distribution in this sandy soil. Full article
(This article belongs to the Special Issue Microbial Diversity: From the Biosphere to the Human Microbiome)
Open AccessArticle Spatial Trends of Genetic Variation of Domestic Ruminants in Europe
Diversity 2010, 2(6), 932-945; doi:10.3390/d2060932
Received: 14 May 2010 / Revised: 1 June 2010 / Accepted: 8 June 2010 / Published: 17 June 2010
Cited by 12 | PDF Full-text (370 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The introduction of livestock species in Europe has been followed by various genetic events, which created a complex spatial pattern of genetic differentiation. Spatial principal component (sPCA) analysis and spatial metric multidimensional scaling (sMDS) incorporate geography in multivariate analysis. This method was [...] Read more.
The introduction of livestock species in Europe has been followed by various genetic events, which created a complex spatial pattern of genetic differentiation. Spatial principal component (sPCA) analysis and spatial metric multidimensional scaling (sMDS) incorporate geography in multivariate analysis. This method was applied to three microsatellite data sets for 45 goat breeds, 46 sheep breeds, and 101 cattle breeds from Europe, Southwest Asia, and India. The first two sPCA coordinates for goat and cattle, and the first sPCA coordinate of sheep, correspond to the coordinates of ordinary PCA analysis. However, higher sPCA coordinates suggest, for all three species, additional spatial structuring. The goat is the most geographically structured species, followed by cattle. For all three species, the main genetic cline is from southeast to northwest, but other geographic patterns depend on the species. We propose sPCA and sMDS to be useful tools for describing the correlation of genetic variation with geography. Full article
(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)
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Review

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Open AccessReview Italian Common Bean Landraces: History, Genetic Diversity and Seed Quality
Diversity 2010, 2(6), 837-862; doi:10.3390/d2060837
Received: 14 April 2010 / Revised: 6 May 2010 / Accepted: 12 May 2010 / Published: 27 May 2010
Cited by 14 | PDF Full-text (612 KB) | HTML Full-text | XML Full-text
Abstract
The long tradition of common bean cultivation in Italy has allowed the evolution of many landraces adapted to restricted areas. Nowadays, in response to market demands, old landraces are gradually being replaced by improved cultivars. However, landraces still survive in marginal areas [...] Read more.
The long tradition of common bean cultivation in Italy has allowed the evolution of many landraces adapted to restricted areas. Nowadays, in response to market demands, old landraces are gradually being replaced by improved cultivars. However, landraces still survive in marginal areas of several Italian regions. Most of them appear severely endangered with risk of extinction due to the advanced age of the farmers and the socio-cultural context where they are cultivated. The present contribution is an overview of the state of the art about the knowledge of Italian common bean germplasm, describing the most important and recent progresses made in its characterization, including genetic diversity and nutritional aspects. Full article
(This article belongs to the Special Issue Assessment of Plant Genetic Diversity)
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Open AccessReview Using Molecular-Assisted Alpha Taxonomy to Better Understand Red Algal Biodiversity in Bermuda
Diversity 2010, 2(6), 946-958; doi:10.3390/d2060946
Received: 4 May 2010 / Revised: 14 May 2010 / Accepted: 13 June 2010 / Published: 17 June 2010
Cited by 15 | PDF Full-text (240 KB) | HTML Full-text | XML Full-text
Abstract
Molecular-assisted alpha taxonomy has recently become an effective practice in reassessing biodiversity and floristics for a variety of different organisms. This paper presents a series of examples that have been drawn from biodiversity work being carried out on the marine red algae [...] Read more.
Molecular-assisted alpha taxonomy has recently become an effective practice in reassessing biodiversity and floristics for a variety of different organisms. This paper presents a series of examples that have been drawn from biodiversity work being carried out on the marine red algae of Bermuda. Molecular sequencing of DNA from Bermuda samples has already begun to greatly alter the makeup of the flora as it was known just decades ago, and will help set a new database for future comparison as climate change affects species composition in the islands. Full article
(This article belongs to the Special Issue Biological Diversity Assessed by Molecular Methods)

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